There was a firefight and heavy casualties were suffered by the NSCN-K, tweeted the Eastern Command.
Reports say Indian commandos exited the operation zone safely. The army has denied reports that its soldiers crossed over the border.
In surgical strikes against Pakistan a year ago, Indian army soldiers had crossed the Line of Control and targeted terror staging areas.
Two years ago, the army attacked separatist rebels just over the border with Myanmar in a rare cross-border strike that the government said showed its resolve to fight terrorism beyond the country’s borders.
The raid was carried out in retaliation for the killing of 20 soldiers in an ambush in Manipur.
The mountainous northeast which borders China, Bhutan, Bangladesh and Myanmar, is home to dozens of insurgent groups.
For decades, soldiers have been deployed in the region but they are not known to have crossed borders even though the military says rebels have sanctuaries in Myanmar, Bangladesh and Bhutan.
At the time, Union Minister Rajyavardhan Singh Rathore had confirmed the strike, saying the government had taken the bold step to target militant camps.
He also told NDTV it was a signal to neighbours that India will not tolerate terror attacks from across its borders.
“It is undoubtedly a message to all nations that harbour any intentions – be it the west or the specific country we went into right now. Even if there are groups within countries that harbour terror intentions, we will choose the time and the place of hitting them.”